Sherekhan

Online analysis tool

Homepage

Fitting functions

Use relax script to create input file

# Create the 'rx' data pipe.
pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')

# The type of experiment
relax_disp.exp_type(exp_type='cpmg fixed')

# Read the sequence from file
sequence.read(file='table_ser_files_model.txt',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)

# Read the intensities from columns
spectrum.read_intensities(file='table_ser_files_model.txt',
dir=None, spectrum_id='0_2', heteronuc='N', proton='HN', int_method='point sum', int_col=(6), spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None)
relax_disp.cpmg_frq(spectrum_id='0_2', cpmg_frq=40.0)
relax_disp.relax_time(spectrum_id='0_2', time=0.05)
spectrometer.frequency(id='0_2', frq=750.0614444, units='MHz')

### Repeat for loading all intensity files

# Replicated spectrums
spectrum.replicated(spectrum_ids=['0_2','7_2','14_2',])
spectrum.replicated(spectrum_ids=['15_14','16_14','20_14',])
spectrum.replicated(spectrum_ids=['3_30','8_30','17_30',])
spectrum.replicated(spectrum_ids=['9_46','19_46','22_46',])
# Spin isotope
spin.isotope(isotope='15N', spin_id='@N*', force=True)

# Make error analysis
spectrum.error_analysis(subset=['0_2', '1_0', '2_8', '3_30', '4_4', '5_42', '6_6', '7_2', '8_30',
 '9_46', '10_10', '11_18', '12_26', '13_38', '14_2', '15_14', '16_14', '17_30', '18_22', '19_46', '20_14', '21_34', '22_46'])

# The 'R2eff' model
pipe.copy(pipe_from='origin rx', pipe_to='R2eff', bundle_to='rx')
pipe.switch(pipe_name='R2eff')
relax_disp.select_model(model='R2eff')
calc(verbosity=1)

# Cluster all spin, and export to sherekhan
relax_disp.cluster(cluster_id='Sherekhan', spin_id=None)
relax_disp.sherekhan_input(force=True, spin_id=None)